Usage: @fast_roi <-region REGION1> [<-region REGION2> ...]
                     <-base TLRC_BASE> <-anat ANAT>
                     <-roi_grid GRID >
                     <-prefix PREFIX >
                     [-time] [-twopass] [-help]
Creates Atlas-based ROI masked in ANAT's original space.
The script is meant to work rapidly for realtime fmri applications
  -region REGION: Symbolic atlas-based region name.
                  See whereami -help for details.
                 You can use repeated instances of this option
                 to specify a mask of numerous regions.
                 Each region is assigned a power of 2 integer
                 in the output mask
  -drawn_roi ROI+tlrc: A user drawn ROI in standard (tlrc) space.
                       This ROI gets added with the REGION roi.

  -anat ANAT: Anat is the volume to be put in std space. It does not
              need to be a T1 weighted volume but you need to choose
              a similarly weighted TLRC_BASE.
              If ANAT is already in TLRC space then there is no need
              for -base option below.
  -anat_ns ANAT: Same as above, but it indicates that the skull
                 has been removed already.
  -base TLRC_BASE:  Name of reference TLRC volume. See @auto_tlrc
                    for more details on this option. Note that
                    for the purposes of speeding up the process,
                    you might want to create a lower resolution
                    version of the templates in the AFNI. In the
                    example shown below, TT_N27_r2+tlrc was created
           3dresample  -dxyz 2 2 2 -rmode Li -prefix ./TT_N27_r2 \
                       -input /home/afniHQ/afni.build/pub.dist/bin/linux_ubuntu_16_64/TT_N27+tlrc.
                    where TT_N27+tlrc is usually in the directory
                    under which afni resides.
  -roi_grid GRID: The volume that defines the final ROI's grid.
  -prefix PREFIX: PREFIX is used to tag the names the ROIs output.
  -time: A flag to make the script output elapsed time reports.
  -twopass: Make TLRC transformation more robust. Use it if TLRC
            transform step fails.
  -help: Output this message.

The ROI of interest is in a volume called ROI.PREFIX+orig.

The script follows the following steps:
  1- Strip skull off of ANAT+orig
     Output is called nosk.ANAT+orig and is reused if present.
  2- Transform nosk.ANAT+orig to TLRC space.
     Output is called nosk.ANAT+tlrc and is reused if present.
  3- Create ROI in TLRC space using 3dcalc.
     Output is ROIt.PREFIX+tlrc and is overwritten if present.
  4- Create ROI in GRID's orig space using 3dFractionize.
     Output is ROI.PREFIX+orig and is overwritten if present.

Examples ( require AFNI_data3/afni, and
           3dresample's output from command shown above):
     @fast_roi  -region CA_N27_ML::Hip -region CA_N27_ML::Amygda \
                 -base TT_N27_r2+tlrc. -anat anat1+orig.HEAD  \
                 -roi_grid epi_r1+orig -prefix toy -time

    If you want another ROI given the same -anat and -base volumes:
     @fast_roi  -region CA_N27_ML::Superior_Temporal_Gyrus \
                 -region CA_N27_ML::Putamen \
                 -base TT_N27_r2+tlrc. -anat anat1+orig.HEAD  \
                 -roi_grid epi_r1+orig -prefix toy -time